Computational Proteomics Training European Innovative Network

Project Information

PROTrEIN

Grant agreement ID: 956148

DOI

10.3030/956148

Project closed

EC signature date 18 August 2020

Start date 1 January 2021

End date 31 December 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 3 917 904,12

EU contribution

€ 3 917 904,12

Coordinated by

FUNDACIO CENTRE DE REGULACIO GENOMICA
Spain

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (6)

Mid-term report on dissemination activities

Midterm report on dissemination activities

Report on Wikipedia editathon and blog site
Report on organised training activities year 1+2

Report on organised training activities year 12

Final report on dissemination activities
Report on Advertisement of vacancies in media

Report on Advertisement of vacancies in media.

Report on organised training activities year 3+4

Other (6)

Open-source tool for the real-time control of mass spectrometry experiments
Release of a new version of MaxQuant and Perseus software suites
Final PROTrEIN Symposium
New file format including ion mobility data to be incorporated into standard proteomics workflows
Web-interface to access the developed learning tools and re-scoring mechanism for crosslinked peptides
PROTrEIN (art) installation

Open Research Data Pilot (1)

Data Management Plan (DMP)

Data Management Plan DMP

Websites, patent fillings, videos etc. (1)

Project website and social media accounts

Publications

Peer reviewed articles (11)

Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit

Author(s): Mario Picciani, Wassim Gabriel, Victor‐George Giurcoiu, Omar Shouman, Firas Hamood, Ludwig Lautenbacher, Cecilia Bang Jensen, Julian Müller, Mostafa Kalhor, Armin Soleymaniniya, Bernhard Kuster, Matthew The, Mathias Wilhelm
Published in: PROTEOMICS, Issue 24, 2024, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202300112

Proteomic Profiling Towards a Better Understanding of Genetic Based Muscular Diseases: The Current Picture and a Look to the Future

Author(s): Marc Pauper, Andreas Hentschel, Malte Tiburcy, Sergi Beltran, Tobias Ruck, Ulrike Schara-Schmidt, Andreas Roos
Published in: Biomolecules, Issue 15, 2025, Page(s) 130, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom15010130

Assessment and Prediction of Human Proteotypic Peptide Stability for Proteomics Quantification

Author(s): Cristina Chiva, Zahra Elhamraoui, Amanda Solé, Marc Serret, Mathias Wilhelm, Eduard Sabidó
Published in: Analytical Chemistry, Issue 95, 2023, Page(s) 13746-13749, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.3c02269

OpenMS WebApps: Building User-Friendly Solutions for MS Analysis

Author(s): Tom David Müller, Arslan Siraj, Axel Walter, Jihyung Kim, Samuel Wein, Johannes von Kleist, Ayesha Feroz, Matteo Pilz, Kyowon Jeong, Justin Cyril Sing, Joshua Charkow, Hannes Luc Röst, Timo Sachsenberg
Published in: Journal of Proteome Research, Issue 24, 2025, Page(s) 940-948, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.4c00872

Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links

Author(s): Arslan Siraj, Robbin Bouwmeester, Arthur Declercq, Luisa Welp, Aleksandar Chernev, Alexander Wulf, Henning Urlaub, Lennart Martens, Sven Degroeve, Oliver Kohlbacher, Timo Sachsenberg
Published in: PROTEOMICS, Issue 24, 2024, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202300144

OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data

Author(s): Julianus Pfeuffer, Chris Bielow, Samuel Wein, Kyowon Jeong, Eugen Netz, Axel Walter, Oliver Alka, Lars Nilse, Pasquale Domenico Colaianni, Douglas McCloskey, Jihyung Kim, George Rosenberger, Leon Bichmann, Mathias Walzer, Johannes Veit, Bertrand Boudaud, Matthias Bernt, Nikolaos Patikas, Matteo Pilz, Michał Piotr Startek, Svetlana Kutuzova, Lukas Heumos, Joshua Charkow, Justin Cyril Sing, Ayesha
Published in: Nature Methods, Issue 21, 2024, Page(s) 365-367, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-024-02197-7

MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0

Author(s): Louise Marie Buur, Arthur Declercq, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer, Ralf Gabriels
Published in: Journal of Proteome Research, 2024, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.26434/chemrxiv-2023-rvr9n

Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification

Author(s): Mostafa Kalhor, Joel Lapin, Mario Picciani, Mathias Wilhelm
Published in: Molecular & Cellular Proteomics, Issue 23, 2024, Page(s) 100798, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2024.100798

Theoretical Assessment of Indistinguishable Peptides in Mass Spectrometry-Based Proteomics

Author(s): Zahra Elhamraoui, Eva Borràs, Mathias Wilhelm, Eduard Sabidó
Published in: Analytical Chemistry, Issue 96, 2024, Page(s) 15829-15833, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.4c02803

How to deal with internal fragment ions?

Author(s): Arthur Grimaud, Masa Babovic, Frederik Haugaard Holck, Ole N. Jensen, Veit Schwämmle
Published in: Molecular & Cellular Proteomics, 2025, Page(s) 100896, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2024.100896

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

Author(s): David Bouyssié, Pınar Altıner, Salvador Capella-Gutierrez, José M. Fernández, Yanick Paco Hagemeijer, Peter Horvatovich, Martin Hubálek, Fredrik Levander, Pierluigi Mauri, Magnus Palmblad, Wolfgang Raffelsberger, Laura Rodríguez-Navas, Dario Di Silvestre, Balázs Tibor Kunkli, Julian Uszkoreit, Yves Vandenbrouck, Juan Antonio Vizcaíno, Dirk Winkelhardt, Veit Schwämmle
Published in: Journal of Proteome Research, Issue 23, 2024, Page(s) 418-429, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.3c00636

Conference proceedings (1)

Extended Reality for Public Understanding of Science: A Systematic Literature Review

Author(s): Prajwal DSouza, Nikoletta-Zampeta Legaki, Daniel Fernández Galeote, Juho Hamari
Published in: Proceedings of the 27th International Academic Mindtrek Conference, 2024, Page(s) 168-175
Publisher: ACM
DOI: 10.1145/3681716.3681734